GEO series
Zinc finger homeobox-3 (ZFHX3) exerts genome-wide regulation of dailygene expression in the suprachiasmatic nucleus [RNA-seq]
GSE261429
Mus musculus (mouse)
RNA-seq (gene expression)
62 samples
Submitted 2025/03/01
Platform GPL24247
At a glance
RNA-seq (gene expression) · mouse · 62 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 62 samples: 17 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Zinc finger homeobox-3 (ZFHX3) orchestrates genome-wide daily gene expression in the suprachiasmatic nucleuseLife · 2025
Summary (written by the submitters)
The mammalian suprachiasmatic nucleus (SCN), situated in the ventral hypothalamus, directs daily cellular and physiological 24-hr rhythms across the body. The cell-autonomous timing mechanism is based on a self-sustaining transcriptional-translational feedback loop (TTFL) that in turn co-ordinates the expression of clock-controlled genes (CCGs) that direct circadian programmes of SCN cellular activity.
Read the full summary ↓
In the mouse, the transcription factor, ZFHX3 (zinc finger homeobox-3), is necessary for the development of the SCN and influences circadian behaviour in the adult. The molecular mechanisms by which ZFHX3 affects the SCN at transcriptome and genome levels are, however, poorly defined. Here, we used chromatin immunoprecipitation (ChIP-seq) to map the genomic localization of ZFHX3 sites in the SCN. In parallel, we conducted a comprehensive SCN RNA sequencing at six distinct times-of-day, and then compared the transcriptional profile between the control and ZFHX3-conditional null mutants. We show that the genome wide occupancy of ZFHX3 occurs predominantly around the gene transcription start site (TSS), co-localizing with the known histone modifications, and preferentially partnering with the core-clock TFs (CLOCK, BMAL1) to regulate the clock gene(s) transcription. Correspondingly, we show that the conditional loss of ZFHX3 in the adult has a dramatic effect on the SCN transcriptome, reducing the level of neuropeptides-encoding transcripts and abolishing rhythmic (24-h) oscillation of the clock TF, Bmal1. In addition, various TTFL genes and CCGs exhibited altered circadian expression profiles, consistent with the advanced daily behaviour under 12hr light- 12hr dark conditions. Taken together, these findings reveal the extensive genome-wide regulation conferred by ZFHX3 in the central clock that orchestrates daily timekeeping in mammals.
Published in
Bafna A, Banks G, Vasilyev V et al.
· eLife 2025
· PMID 40117332
· doi:10.7554/eLife.102019
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261429_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1086932 and SRA study SRP497273. Searching any of these in the dataset finder brings you back here.
Study design
17 conditions, mostly with about 4 replicates each
SCN, control1, 2hours, ×4
SCN, control1, 6hours, ×4
SCN, control1, 10hours, ×4
SCN, control1, 14hours, ×4
SCN, control1, 18hours, ×4
SCN, control1, 22hours, ×4
SCN, mutant, 2hours, ×4
SCN, mutant, 6hours, ×4
+10 more
Supports a case/control comparison: 24 samples read as cases, 38 as controls.
How we read this: 17 replicated groups read from 62 sample titles; they account for 61 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM8143850 SCN, control1, 2hours, rep1 SCN, control1, 2hours,
- GSM8143851 SCN, control1, 2hours, rep2 SCN, control1, 2hours,
- GSM8143852 SCN, control1, 2hours, rep3 SCN, control1, 2hours,
- GSM8143853 SCN, control1, 2hours, rep4 SCN, control1, 2hours,
- GSM8143854 SCN, control1, 6hours, rep1 SCN, control1, 6hours,
- GSM8143855 SCN, control1, 6hours, rep2 SCN, control1, 6hours,
- GSM8143856 SCN, control1, 6hours, rep3 SCN, control1, 6hours,
- GSM8143857 SCN, control1, 6hours, rep4 SCN, control1, 6hours,
- GSM8143858 SCN, control1, 10hours, rep1 SCN, control1, 10hours,
- GSM8143859 SCN, control1, 10hours, rep2 SCN, control1, 10hours,
- GSM8143860 SCN, control1, 10hours, rep3 SCN, control1, 10hours,
- GSM8143861 SCN, control1, 10hours, rep4 SCN, control1, 10hours,
- GSM8143862 SCN, control1, 14hours, rep1 SCN, control1, 14hours,
- GSM8143863 SCN, control1, 14hours, rep2 SCN, control1, 14hours,
- GSM8143864 SCN, control1, 14hours, rep3 SCN, control1, 14hours,
- GSM8143865 SCN, control1, 14hours, rep4 SCN, control1, 14hours,
- GSM8143866 SCN, control1, 18hours, rep1 SCN, control1, 18hours,
- GSM8143867 SCN, control1, 18hours, rep2 SCN, control1, 18hours,
- GSM8143868 SCN, control1, 18hours, rep3 SCN, control1, 18hours,
- GSM8143869 SCN, control1, 18hours, rep4 SCN, control1, 18hours,
- GSM8143870 SCN, control1, 22hours, rep1 SCN, control1, 22hours,
- GSM8143871 SCN, control1, 22hours, rep2 SCN, control1, 22hours,
- GSM8143872 SCN, control1, 22hours, rep3 SCN, control1, 22hours,
- GSM8143873 SCN, control1, 22hours, rep4 SCN, control1, 22hours,
- GSM8143874 SCN, mutant, 2hours, rep1 SCN, mutant, 2hours,
- GSM8143875 SCN, mutant, 2hours, rep2 SCN, mutant, 2hours,
- GSM8143876 SCN, mutant, 2hours, rep3 SCN, mutant, 2hours,
- GSM8143877 SCN, mutant, 2hours, rep4 SCN, mutant, 2hours,
- GSM8143878 SCN, mutant, 6hours, rep1 SCN, mutant, 6hours,
- GSM8143879 SCN, mutant, 6hours, rep2 SCN, mutant, 6hours,
- GSM8143880 SCN, mutant, 6hours, rep3 SCN, mutant, 6hours,
- GSM8143881 SCN, mutant, 6hours, rep4 SCN, mutant, 6hours,
- GSM8143882 SCN, mutant, 10hours, rep1 SCN, mutant, 10hours,
- GSM8143883 SCN, mutant, 10hours, rep2 SCN, mutant, 10hours,
- GSM8143884 SCN, mutant, 10hours, rep3 SCN, mutant, 10hours,
- GSM8143885 SCN, mutant, 10hours, rep4 SCN, mutant, 10hours,
- GSM8143886 SCN, mutant, 14hours, rep1 SCN, mutant, 14hours,
- GSM8143887 SCN, mutant, 14hours, rep2 SCN, mutant, 14hours,
- GSM8143888 SCN, mutant, 14hours, rep3 SCN, mutant, 14hours,
- GSM8143889 SCN, mutant, 14hours, rep4 SCN, mutant, 14hours,
+ 22 more — browse all 62 samples with per-sample file links →
Datasets on a similar topic
- GSE261795 Zinc finger homeobox-3 (ZFHX3) exerts genome-wide regulation of dailygene expression in the suprachiasmatic nucleus 65 samples shares homeobox-3, zfhx3, suprachiasmatic, genome-wide, dailygene, finger, exerts
- GSE243373 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq] 15 samples shares genome-wide, rna-seq
- GSE202584 Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation [Hoxb8-FL RNA-Seq] 15 samples shares genome-wide, rna-seq
- GSE252758 OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide (RNA-Seq) 4 samples shares genome-wide, rna-seq
- GSE262791 LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos 468 samples shares genome-wide, rna-seq
- GSE198005 Genome-wide bisulfite sequencing (GWBS) and RNA-seq in hippocampus of Neil1- and Neil2 deficient mice 16 samples shares genome-wide, rna-seq
- GSE241542 A phosphate transporter in VIPergic neurons of the suprachiasmatic nucleus gates locomotor activity during the light/dark transition in mice 298 samples shares suprachiasmatic
- GSE285351 Genome-wide in vivo CRISPR screens identify GATOR1 as a potent tumor suppressor in MYC-driven lymphomagenesis 35 samples shares genome-wide
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.